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On the evolution and genetic diversity of the bread wheat D genome

Molecular Plant 2024年第11期17卷 1672-1686页

作者： Zihao Wang Wenxi Wang Yachao He Xiaoming Xie Zhengzhao Yang Xiaoyu Zhang Jianxia Niu Huiru Peng yingyin yao Chaojie Xie Mingming Xin Zhaorong Hu Qixin Sun Zhongfu Ni Weilong Guo Frontiers Science Center for Molecular Design Breeding Key Laboratory of Crop Heterosis and UtilizationBeijing Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijing 100193China Sanya Institute of China Agricultural University Sanya 572025China

Bread wheat(Triticum aestivum)became a globally dominant crop after incorporating the D genome from the donor species Aegilops tauschii,but the evolutionary history that shaped the D genome during this process remains to be ***,we propose a renewed evolutionary model linking *** and the hexaploid wheat D genome by constructing an ancestral haplotype map covering 762 *** and hexaploid wheat *** dissected the evolutionary trajectories of *** lineages and reported a few independent intermediate accessions,demonstrating that low-frequency intersublineage gene flow had enriched the diversity of *** discovered that the D genome of hexaploid wheat was inherited from a unified ancestral template,but with a mosaic composition that was highly mixed and derived mainly from three *** L2 sublineages located in the Caspian coastal *** result suggests that early agricultural activities facilitated innovations in D-genome composition and finalized the success of *** found that the majority(51.4%)of genetic diversity was attributed to novel mutations absent in ***,and we identified large *** introgressions from various lineages,which expanded the diversity of the wheat D genome and introduced beneficial *** work sheds light on the process of wheat hexaploidization and highlights the evolutionary significance of the multi-layered genetic diversity of the bread wheat D genome.

关键词： wheat Aegilops tauschii D genome genetic diversity evolution

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Paternally imprinted LATE-FLOWERING2 transcription factor contributes to paternal-excess interploidy hybridization barriers in wheat∞

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Journal of Integrative Plant Biology 2023年第12期65卷 2587-2603页

作者： Guanghui Yang Man Feng Kuohai Yu Guangxian Cui Yan Zhou Lv Sun Lulu Gao Yumei Zhang Huiru Peng yingyin yao Zhaorong Hu Vincenzo Rossi Ive De Smet Zhongfu Ni Qixin Sun Mingming Xin State Key Laboratory for Agrobiotechnology Key Laboratory of Crop Heterosis Utilization(MOE)Beijing Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijing 100193China Qingdao Agricultural University Qingdao 266109China Council for Agricultural Research and Economics Research Centre for Cereal and Industrial CropsBergamo 24126Italy Department of Plant Biotechnology and Bioinformatics Ghent UniversityGhent B‐9052Belgium VIB Center for Plant Systems Biology Ghent B‐9052Belgium

Interploidy hybridization between hexaploid and tetraploid genotypes occurred repeatedly during genomic introgression events throughout wheat evolution,and is commonly employed in wheat breeding *** wheat usually serves as maternal parent because the reciprocal cross generates progeny with severe defects and poor seed germination,but the underlying mechanism is poorly ***,we performed detailed analysis of phenotypic variation in endosperm between two interploidy reciprocal crosses arising from tetraploid(Triticum durum,AABB)and hexaploid wheat(Triticum aestivum,AABBDD).In the paternal‐versus the maternal‐excess cross,the timing of endosperm cellularization was delayed and starch granule accumulation in the endosperm was repressed,causing reduced germination *** expression profiles of genes involved in nutrient metabolism differed strongly between these endosperm ***,expression patterns of parental alleles were dramatically disturbed in interploidy versus intraploidy crosses,leading to increased number of imprinted *** endosperm‐specific TaLFL2 showed a paternally imprinted expression pattern in interploidy crosses partially due to allele‐specific DNA *** TaLFL2 binds to and represses a nutrient accumulation regulator TaNAC019,leading to reduced storage protein and starch accumulation during endosperm development in paternal‐excess cross,as confirmed by interploidy crosses between tetraploid wild‐type and clustered regularly interspaced palindromic repeats(CRISPR)–CRISPR‐associated protein 9 generated hexaploid *** findings reveal a contribution of genomic imprinting to paternal‐excess interploidy hybridization barriers during wheat evolution history and explains why experienced breeders preferentially exploit maternal‐excess interploidy crosses in wheat breeding programs.

关键词： imprinting interploidy cross wheat

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TaACTIN7-D regulates plant height and grain shape in bread wheat

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Journal of Genetics and Genomics 2023年第11期50卷 895-908页

作者： Xiongtao Li Beilu Cao Dejie Du Long Song Lulu Tian Xiaoming Xie Zhaoyan Chen Yanpeng Ding Xuejiao Cheng yingyin yao Weilong Guo Zhenqi Su Qixin Sun Zhongfu Ni Lingling Chai Jie Liu Frontiers Science Center for Molecular Design Breeding China Agricultural UniversityBeijing 100193China State Key Laboratory for Crop Genetics and Germplasm Enhancement Nanjing Agricultural UniversityNanjingJiangsu 210095China

Exploitation of new gene resources and genetic networks contributing to the control of crop yield-related traits,such as plant height,grain size,and shape,may enable us to breed modern high-yielding wheat varieties through molecular *** this study,via ethylmethanesulfonate mutagenesis,we identify a wheat mutant plant,mu-597,that shows semi-dwarf plant architecture and round grain *** bulked segregant RNA-seq and map-based cloning,the causal gene for the semi-dwarf phenotype of mu-597 is *** find that a single-base mutation in the coding region of TaACTIN7-D(TaACT7-D),leading to a Gly-to-Ser(G65S)amino acid mutation at the 65th residue of the deduced TaACT7-D protein,can explain the semi-dwarfism and round grain shape of *** evidence shows that the G65S mutation in TaACT7-D hinders the polymerization of actin from monomeric(G-actin)to filamentous(F-actin)status while attenuates wheat responses to multiple phytohormones,including brassinosteroids,auxin,and ***,these findings not only define a new semi-dwarfing gene resource that can be potentially used to design plant height and grain shape of bread wheat but also establish a direct link between actin structure modulation and phytohormone signal transduction.

关键词： Wheat(Triticum aestivum L.) Plant height Grain shape TaACT7-D Phytohormone signaling

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A k-mer-based pangenome approach for cataloging seed-storage-protein genes in wheat to facilitate genotype-to-phenotype prediction and improvement of end-use quality

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Molecular Plant 2024年第7期17卷 1038-1053页

作者： Zhaoheng Zhang Dan Liu Binyong Li Wenxi Wang Jize Zhang Mingming Xin Zhaorong Hu Jie Liu Jinkun Du Huiru Peng Chenyang Hao Xueyong Zhang Zhongfu Ni Qixin Sun Weilong Guo yingyin yao Frontiers Science Center for Molecular Design Breeding Key Laboratory of Crop Heterosis and Utilization(MOE)and Bejing Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijing100193China Key Laboratory of Crop Gene Resources and Breeding Institute of Crop ScienceChinese Academy of Agricultural SciencesBejingChina

Wheat is a staple foodfor more than 35%of the world's population,with wheatflourused to make hundreds of baked *** end-use quality is a major breeding target;however,improving it is especially time-consuming and ***,genes encoding seed-storage proteins(ssPs)form multigene families and are repetitive,with gaps commonplace in several genome *** overcome these barriers and efficiently identify superior wheat SSP alleles,we developed"PanSK"(Pan-SSP k-mer)for genotype-to-phenotype prediction based on an SsP-based pangenome *** uses 29-mer sequences that represent each ssP gene at the pangenomic level to reveal untapped diversity across landraces and modern ***-wide association studies with k-mers identified 23 Ssp genes associated with end-use quality that represent novel targets for *** evaluated the effect of rye secalin genes on end-use quality and found that removal of w-secalins from 1BL/1RS wheat translocation lines is associated with enhanced end-use ***,using machine-learning-based prediction inspired by PanSK,we predicted the quality phenotypes with high accuracy from genotypes *** study provides an effective approach for genome design based on ssP genes,enabling the breeding of wheat varieties with superior processing capabilities and improved end-use quality.

关键词： wheat seed-storage protein end-use quality k-mer pangenome genomic prediction

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TaANR1-TaMADS25 module regulates lignin biosynthesis and root development in wheat(Triticum aestivum L.)

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Journal of Genetics and Genomics 2023年第11期50卷 917-920页

作者： Weiya Xu Yongming Chen Bin Liu Qiuyuan Li Yilan Zhou Xuanshuang Li Weilong Guo Zhaorong Hu Zhenshan Liu Mingming Xin yingyin yao Mingshan You Huiru Peng Zhongfu Ni Jiewen Xing Key Laboratory of Crop Heterosis and Utilization(MOE) Beijing Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijing 100193China State Key Laboratory of Crop Stress Biology for Arid Areas College of AgronomyNorthwest A&F UniversityYanglingShaanxi 712100China

Common wheat is a staple food for 35%of the global population,therefore increasing wheat yield in an ever-changing environment is essential for food security in the present day(Peng et al.,2011).Root system is responsible for water and nutrient acquisition,thus crucial for competitive fitness and crop yield in challenging environments(Karlova et al.,2021;Liu et al.,2022).Over the past decades,extensive research has focused on identifying genes accountable for root growth and development in plants(Rogers and Benfey,2015).However,only a limited number of genes have been cloned in wheat(Li et al.,2021).

关键词： wheat environments Root

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Cloning and characterization of an up-regulated GA 20-oxidase gene in hybrid maize

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Progress in Natural Science:Materials International 2009年第2期19卷 161-166页

作者： Jinkun Du,yingyin yao,Zhongfu Ni,Qixin Sun Department of Plant Genetics & Breeding and State Key Laboratory for Agrobiotechnology,Key Laboratory of Crop Genomics and Genetic Improvement,Ministry of Agriculture/Beijing Key Laboratory of Crop Genetic Improvement,China Agricultural University,Beijing 100094,China Department of Plant Genetics & Breeding and State Key Laboratory for Agrobiotechnology Key Laboratory of Crop Genomics and Genetic Improvement Ministry of Agriculture/Beijing Key Laboratory of Crop Genetic Improvement China Agricultural University Beijing 100094 China

Previous studies revealed that GA content and metabolism are positively correlated with a faster shoot growth rate of hybrid,and recently,genes participating in both GA biosynthesis and GA response pathways were also found to be differentially expressed between wheat hybrid and its parental inbreds. In this study,an up-regulated GA 20-oxidase gene in a maize hybrid,designated ZmGA20,was cloned. ZmGA20 contains an open reading frame (ORF) encoding 391 amino acid residues. BLASTX searches in GenBank revealed that the ZmGA20 is homologous to the sequences of GA20ox proteins from different species,and analysis also indicated that ZmGA20 had typical features of GA 20-oxidase proteins,including a "LPWKET" sequence. Semi-quantitative RT-PCR analysis showed that ZmGA20 was expressed in different tissues and/or organs. The expression level of ZmGA20 in the hybrid was higher than that in two parents (in roots,leaves,stems and embryo,and ears). The abundance of ZmGA20 transcript was equal to that of the highly expressed parents,which provided molecular evidence for the observed GA content heterosis in maize hybrids.

关键词： GA 20-oxidase Gene expression Maize Heterosis

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Ectopic expression of VRT-A2 underlies the origin of Triticum polonicum and Triticum petropavlovskyi with long outer glumes and grains

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Molecular Plant 2021年第9期14卷 1472-1488页

作者： Jing Liu Zhaoyan Chen Zhihui Wang Zhaoheng Zhang Xiaoming Xie Zihao Wang Lingling Chai Long Song Xuejiao Cheng Man Feng Xiaobo Wang Yanhong Liu Zhaorong Hu Jiewen Xing Zhenqi Su Huiru Peng Mingming Xin yingyin yao Weilong Guo Qixin Sun Jie Liu Zhongfu Ni State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization(MOE)and Beijing Key Laboratory of Crop Genetic Improvement China Agricultural UniversityBeijing 100193P.R.China

Polish wheat (Triticum polonicum) is a unique tetraploid wheat species characterized by an elongated outer glume. The genetic control of the long-glume trait by a single semi-dominant locus, P1 (from Polish wheat), was established more than 100 years ago, but the underlying causal gene and molecular nature remain elusive. Here, we report the isolation of VRT-A2, encoding an SVP-clade MADS-box transcription factor, as the P1 candidate gene. Genetic evidence suggests that in T. polonicum, a naturally occurring sequence rearrangement in the intron-1 region of VRT-A2 leads to ectopic expression of VRT-A2 in floral organs where the long-glume phenotype appears. Interestingly, we found that the intron-1 region is a key ON/OFF molecular switch for VRT-A2 expression, not only because it recruits transcriptional repressors, but also because it confers intron-mediated transcriptional enhancement. Genotypic analyses using wheat accessions indicated that the P1 locus is likely derived from a single natural mutation in tetraploid wheat, which was subsequently inherited by hexaploid T. petropavlovskyi. Taken together, our findings highlight the promoter-proximal intron variation as a molecular basis for phenotypic differentiation, and thus species formation in Triticum plants.

关键词： long glume P1 species differentiation T.polonicum VRT-A2

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The TaTCP4/10-B1 cascade regulates awn elongation in wheat(Triticum aestivum L.)

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Plant Communications 2023年第4期4卷 255-270页

作者： Wensheng Ke Jiewen Xing Zhaoyan Chen Yidi Zhao Weiya Xu Lulu Tian Jinquan Guo Xiaoming Xie Dejie Du Zihao Wang Yufeng Li Jin Xu Mingming Xin Weilong Guo Zhaorong Hu Zhenqi Su Jie Liu Huiru Peng yingyin yao Qixin Sun Zhongfu Ni Frontiers Science Center for Molecular Design Breeding Key Laboratory of Crop Heterosis and Utilization(MOE)Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijing 100193China

Awns are important morphological markers for wheat and exert a strong physiological effect on wheat *** awn elongation suppressor B1 has recently been cloned through association and linkage analysis in ***,the mechanism of awn inhibition centered around B1 remains to be ***,we identified an allelic variant in the coding region of B1 through analysis of re-sequencing data;this variant causes an amino acid substitution and premature termination,resulting in a long-awn *** analysis indicated that B1 inhibited awn elongation by impeding cytokinin-and auxinpromoted cell ***,B1 directly repressed the expression of TaRAE2 and TaLks2,whose orthologs have been reported to promote awn development in rice or *** importantly,we found that TaTCP4 and TaTCP10 synergistically inhibited the expression of B1,and a G-to-A mutation in the B1 promoter attenuated its inhibition by TaTCP4/*** together,our results reveal novel mechanisms of awn development and provide genetic resources for trait improvement in wheat.

关键词： TaTCP4/10 B1 awn length haplotype wheat

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Genomic and genic sequence variation in synthetic hexaploid wheat (AABBDD) as compared to their parental species

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Progress in Natural Science:Materials International 2008年第5期18卷 533-538页

作者： Lihong Nie, Zongfu Han, Lahu Lu, yingyin yao, Qixin Sun, Zhongfu Ni Key Laboratory of Crop Heterosis and Utilization (MOE) and State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Genomics and Genetic Improvement (MOA), Beijing Key Laboratory of Crop Genetic Improvement, Department of Plant Genetics & Breeding, China Agricultural University, Beijing 100094, China Key Laboratory of Crop Heterosis and Utilization (MOE) and State Key Laboratory for Agrobiotechnology Key Laboratory of Crop Genomics and Genetic Improvement (MOA) Beijing Key Laboratory of Crop Genetic Improvement Department of Plant Genetics & Breeding China Agricultural University Beijing 100094 China

In order to understand the genomic changes during the evolution of hexaploid wheat, two sets of synthetic hexaploid wheat from hybridization between maternal tetraploid wheat (AABB) and paternal diploid goat grass (DD) were used for DNA-AFLP and single strand conformation polymorphism (SSCP) analysis to determine the genomic and genic variation in the synthetic hexaploid wheat. Results indicated that more DNA sequences from paternal diploid species were eliminated in the synthetic hexaploid wheat than from maternal tetraploid wheat, suggesting that genome from parental species of lower ploidity tends to be eliminated preferentially. However, sequence variation detected by SSCP procedure was much lower than those detected by DNA-AFLP, which indicated that much less variation in the genic regions occurred in the synthetic hexaploid wheat, and sequence variations detected by DNA-AFLP could be derived mostly from non-coding regions and repetitive sequences. Our results also indicated that sequence variation in 4 genes can be detected in hybrid F1, which suggested that this type of sequence variation could be resulted from distant hybridization. It was interesting to note that 3 out of the 4 genes were mapped and clustered on the long arm of chromosome 2D, which indicated that variation in genic sequences in synthetic hexaploid wheat might not be a randomized process.

关键词： Synthetic hexaploid wheat Polyploidy Genome Sequence variation

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A natural variation in Ribonuclease H-like gene underlies Rht8 to confer“Green Revolution”trait in wheat

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Molecular Plant 2022年第3期15卷 377-380页

作者： Lingling Chai Mingming Xin Chaoqun Dong Zhaoyan Chen Huijie Zhai Junhong Zhuang Xuejiao Cheng Naijiao Wang Jia Geng Xiaobo Wang Ruolin Bian yingyin yao Weilong Guo Zhaorong Hu Huiru Peng Guihua Bai Qixin Sun Zhenqi Su Jie Liu Zhongfu Ni State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization(MOE)and Beijing Key Laboratory of Crop Genetic Improvement China Agricultural UniversityBeijingChina School of Life Science and Technology Henan Institute of Science and TechnologyXinxiangChina Center for Crop Functional Genomics and Molecular Breeding China Agricultural UniversityBeijingChina State Key Laboratory for Crop Genetics and Germplasm Enhancement Nanjing Agricultural UniversityNanjingChina USDA–ARS Hard Winter Wheat Genetics Research UnitManhattanKSUSA

Dear Editor,Introduction of gibberellin(GA)-insensitive Reduced height(Rht)genes,Rht-B1b and Rht-D1b,has resulted in the“Green Revolution”in modern wheat cultivars(Triticum aestivum)that has skyrocketed wheat grain yields worldwide since the 1960s(Peng et al.,1999;Velde et al.,2021).However,Rht-B1b/D1b also reduce coleoptiles,which is undesired in dryland regions where deep planting is essential for seedling establishment(Rebetzke et al.,1999,Rebetzke et al.,2001;Ellis et al.,2004).

关键词： aestivum seedling cultivar

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